- Isis-fish-data-commits - mailman.cloud.codelutin.com

r354 - trunk
by echatellier＠users.forge.codelutin.com April 21, 2015

April 21, 2015

Author: echatellier Date: 2015-04-21 12:44:34 +0000 (Tue, 21 Apr 2015) New Revision: 354 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/354 Log: Prepare next iteration Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2015-04-21 09:20:26 UTC (rev 353) +++ trunk/pom.xml 2015-04-21 12:44:34 UTC (rev 354) @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.4.0.0-rc-1-SNAPSHOT</version> + <version>4.4.0.0-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies>

1 0

r353 - in trunk: . scripts simulators
by echatellier＠users.forge.codelutin.com April 21, 2015

April 21, 2015

Author: echatellier Date: 2015-04-21 09:20:26 +0000 (Tue, 21 Apr 2015) New Revision: 353 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/353 Log: fixes #6194: changement reproduction/recrutement Modified: trunk/pom.xml trunk/scripts/SiMatrix.java trunk/simulators/DefaultSimulator.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2015-04-16 16:43:41 UTC (rev 352) +++ trunk/pom.xml 2015-04-21 09:20:26 UTC (rev 353) @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.4.0.0-SNAPSHOT</version> + <version>4.4.0.0-rc-1-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies> Modified: trunk/scripts/SiMatrix.java =================================================================== --- trunk/scripts/SiMatrix.java 2015-04-16 16:43:41 UTC (rev 352) +++ trunk/scripts/SiMatrix.java 2015-04-21 09:20:26 UTC (rev 353) @@ -29,7 +29,6 @@ import java.util.Collections; import java.util.HashSet; import java.util.List; -import java.util.Set; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; @@ -1351,7 +1350,6 @@ //log.info("Recruitment_1 = " + RecruitmentMatrix); // Pour chaque pas de temps on recupere le recrutement - RecruitmentMatrix.setValue(pop, context.getPopulationMonitor().getRecruitment(step, pop).sumAll()); //log.info("RecruitmentMatrix_2 = " + RecruitmentMatrix); Modified: trunk/simulators/DefaultSimulator.java =================================================================== --- trunk/simulators/DefaultSimulator.java 2015-04-16 16:43:41 UTC (rev 352) +++ trunk/simulators/DefaultSimulator.java 2015-04-21 09:20:26 UTC (rev 353) @@ -382,8 +382,8 @@ // N is reassigned during computation resManager.addResult(step, pop, N); + MatrixND biomass = siMatrix.matrixBiomass(N, pop, step); if (resManager.isEnabled(ResultName.MATRIX_BIOMASS)) { - MatrixND biomass = siMatrix.matrixBiomass(N, pop, step); resManager.addResult(step, pop, biomass); } @@ -433,7 +433,7 @@ // ajout de la matrice R dans le suivi de la pop comme etant // la reproduction pour le mois courant. - popMon.setReproduction(step, pop, R); + popMon.setReproduction(step, pop, N, biomass, R); // recrutement MatrixND recruitment = popMon.getRecruitment(step, pop);

1 0

r352 - in trunk: exports scripts sensitivityexports simulators
by echatellier＠users.forge.codelutin.com April 16, 2015

April 16, 2015

Author: echatellier Date: 2015-04-16 16:43:41 +0000 (Thu, 16 Apr 2015) New Revision: 352 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/352 Log: Add Lbar and recruitment exports Added: trunk/exports/Lbar.java trunk/exports/Recruitment.java trunk/sensitivityexports/SensitivityLbarJanvierY1.java trunk/sensitivityexports/SensitivityRecruitmentY1.java Modified: trunk/scripts/ResultName.java trunk/scripts/SiMatrix.java trunk/scripts/SiMatrixEffortByCell.java trunk/simulators/DefaultSimulator.java Added: trunk/exports/Lbar.java =================================================================== --- trunk/exports/Lbar.java (rev 0) +++ trunk/exports/Lbar.java 2015-04-16 16:43:41 UTC (rev 352) @@ -0,0 +1,90 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2015 Ifremer, CodeLutin + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ +package exports; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +import java.io.Writer; + +import org.nuiton.math.matrix.*; + +import scripts.ResultName; + +import fr.ifremer.isisfish.entities.*; +import fr.ifremer.isisfish.export.Export; +import fr.ifremer.isisfish.types.TimeStep; +import fr.ifremer.isisfish.datastore.SimulationStorage; + +/** + * Population mean length. + * + * Created: 03/2015 + * + * @author lgasche <anonymous(a)labs.libre-entreprise.org> + * @version $Revision$ + */ +public class Lbar implements Export { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(Lbar.class); + + protected String[] necessaryResult = { + ResultName.MATRIX_LBAR + }; + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + + @Override + public String getExportFilename() { + return "Lbar"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String getDescription() { + return "Exporte les longueurs moyennes par pop par zone en tableau avec des lignes pop;zone;date;longueur."; + } + + @Override + public void export(SimulationStorage simulation, Writer out) throws Exception { + for (Population pop : simulation.getParameter().getPopulations()) { + MatrixND mat = simulation.getResultStorage().getMatrix(pop, ResultName.MATRIX_LBAR); + for (MatrixIterator i = mat.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + TimeStep step = (TimeStep) sems[0]; + Zone zone = (Zone) sems[1]; + + double val = i.getValue(); + out.write(pop.getName() + ";" + zone.getName() + ";" + step.getStep() + ";" + val + "\n"); + } + } + } +} Property changes on: trunk/exports/Lbar.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Added: trunk/exports/Recruitment.java =================================================================== --- trunk/exports/Recruitment.java (rev 0) +++ trunk/exports/Recruitment.java 2015-04-16 16:43:41 UTC (rev 352) @@ -0,0 +1,89 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2015 Ifremer, CodeLutin + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ +package exports; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +import java.io.Writer; + +import org.nuiton.math.matrix.*; + +import scripts.ResultName; + +import fr.ifremer.isisfish.entities.*; +import fr.ifremer.isisfish.export.Export; +import fr.ifremer.isisfish.types.TimeStep; +import fr.ifremer.isisfish.datastore.SimulationStorage; + +/** + * Recruitment. + * + * Created: 03/2015 + * + * @author lgasche <anonymous(a)labs.libre-entreprise.org> + * @version $Revision$ + */ +public class Recruitment implements Export { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(Recruitment.class); + + protected String[] necessaryResult = { + ResultName.MATRIX_RECRUITMENT + }; + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + + @Override + public String getExportFilename() { + return "Recruitment"; + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String getDescription() { + return "Exporte le recrutement par pop par en tableau avec des lignes pop;date;recrutement."; + } + + @Override + public void export(SimulationStorage simulation, Writer out) throws Exception { + for (Population pop : simulation.getParameter().getPopulations()) { + MatrixND mat = simulation.getResultStorage().getMatrix(pop, ResultName.MATRIX_RECRUITMENT); + for (MatrixIterator i = mat.iterator(); i.hasNext();) { + i.next(); + Object[] sems = i.getSemanticsCoordinates(); + TimeStep step = (TimeStep) sems[0]; + + double val = i.getValue(); + out.write(pop.getName() + ";" + step.getStep() + ";" + val + "\n"); + } + } + } +} Property changes on: trunk/exports/Recruitment.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Modified: trunk/scripts/ResultName.java =================================================================== --- trunk/scripts/ResultName.java 2014-12-22 10:19:18 UTC (rev 351) +++ trunk/scripts/ResultName.java 2015-04-16 16:43:41 UTC (rev 352) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2014 Ifremer, Code Lutin, Cedric Pineau, Benjamin Poussin + * Copyright (C) 2006 - 2015 Ifremer, Code Lutin, Cedric Pineau, Benjamin Poussin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -112,7 +112,7 @@ * Dimension 4 : Group * Dimension 5 : Zone * - * N'est calculé que si l'effort est calculé par cellule et non par zone. + * N'est calcule que si l'effort est calcule par cellule et non par zone. * @see simulators.SimulatorEffortByCell */ @Doc(value = "do the doc of Result matrixCatchPerStrategyMetPerZoneMet") @@ -137,7 +137,7 @@ * Dimension 4 : Group * Dimension 5 : Zone * - * N'est calculé que si l'effort est calculé par cellule et non par zone. + * N'est calcule que si l'effort est calcule par cellule et non par zone. * @see simulators.SimulatorEffortByCell */ @Doc(value = "do the doc of Result matrixCatchWeightPerStrategyMetPerZoneMet") @@ -188,6 +188,21 @@ */ @Doc(value = "do the doc of Result matrixAbundance") static final public String MATRIX_ABUNDANCE = n("matrixAbundance"); + + /** + * Matrix with two dimensions + * Dimension 1 : TimeStep + * Dimension 2 : Zone (semantics : Dimension 1) + */ + @Doc(value = "do the doc of Result matrixLbar") + static final public String MATRIX_LBAR = n("matrixLbar"); + + /** + * Matrix with one dimension + * Dimension 1 : TimeStep + */ + @Doc(value = "do the doc of Result matrixRecruitment") + static final public String MATRIX_RECRUITMENT = n("matrixRecruitment"); /** * Matrix with three dimensions Modified: trunk/scripts/SiMatrix.java =================================================================== --- trunk/scripts/SiMatrix.java 2014-12-22 10:19:18 UTC (rev 351) +++ trunk/scripts/SiMatrix.java 2015-04-16 16:43:41 UTC (rev 352) @@ -2,7 +2,7 @@ * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2014 Ifremer, Code Lutin, Benjamin Poussin + * Copyright (C) 2006 - 2015 Ifremer, Code Lutin, Benjamin Poussin * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -273,7 +273,6 @@ * @param N l'abondance sous forme de matrice 2D [class x zone] * @param pop * @param step - * @param matrixCatchRatePerStrategyMet * @return * @throws TopiaException * @throws IsisFishException @@ -306,7 +305,6 @@ * * @param pop * @param step - * @param matrixFishingMortality * @return * @throws TopiaException * @throws IsisFishException @@ -894,7 +892,6 @@ * @param N * @param pop * @param step - * @param matrixFishingMortality * @return * @throws IsisFishException * @throws TopiaException @@ -1289,4 +1286,76 @@ return result; } + + /** + * Permet de calculer la longueur moyenne (Lbar) d'une population. + * + * @param step + * @param pop + * @param N + * @return + */ + public MatrixND Lbar(TimeStep step, Population pop, MatrixND N) throws TopiaException { + MatrixND LbarMatrix = N.copy(); + LbarMatrix.setName(ResultName.MATRIX_LBAR); + //log.info("Lbar_1 = " + LbarMatrix); + + List<PopulationGroup> groups = pop.getPopulationGroup(); + List<Zone> zones = pop.getPopulationZone(); + + // On multiplie l'abondance de chaque groupe par la taille de ce groupe + + // On somme sur les groupes + + // On utilise divise la valeur obtenue par l'abondance totale + + for (PopulationGroup group : groups) { + for (Zone zn : zones) { + LbarMatrix.setValue(group, zn, LbarMatrix.getValue(group, zn) * group.getLength()); + } + } + + LbarMatrix = LbarMatrix.sumOverDim(0); // Somme sur les groupes + LbarMatrix = LbarMatrix.reduce(); + //log.info("LbarMatrix_2 = " + LbarMatrix); + + MatrixND matAB = N.copy(); + matAB = matAB.sumOverDim(0); + matAB = matAB.reduce(); + //log.info("matAB = " + matAB); + + for (Zone zn : zones) { + LbarMatrix.setValue(zn, LbarMatrix.getValue(zn) / matAB.getValue(zn)); + } + + //log.info("LbarMatrix_3 = " + LbarMatrix); + + return LbarMatrix; + } + + /** + * Permet de sortir le recrutement par pas de temps. + * @param step + * @param pop + * @return + */ + public MatrixND Recruitment(TimeStep step, Population pop) throws TopiaException { + + List<Population> populations = Collections.singletonList(pop); + + MatrixND RecruitmentMatrix = MatrixFactory.getInstance().create( + ResultName.MATRIX_RECRUITMENT, + new List[]{populations}, // + new String[]{n("Population")}); + + //log.info("Recruitment_1 = " + RecruitmentMatrix); + + // Pour chaque pas de temps on recupere le recrutement + + RecruitmentMatrix.setValue(pop, context.getPopulationMonitor().getRecruitment(step, pop).sumAll()); + + //log.info("RecruitmentMatrix_2 = " + RecruitmentMatrix); + + return RecruitmentMatrix; + } } Modified: trunk/scripts/SiMatrixEffortByCell.java =================================================================== --- trunk/scripts/SiMatrixEffortByCell.java 2014-12-22 10:19:18 UTC (rev 351) +++ trunk/scripts/SiMatrixEffortByCell.java 2015-04-16 16:43:41 UTC (rev 352) @@ -1,3 +1,24 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2015 Ifremer, Code Lutin, Benjamin Poussin + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ package scripts; import static org.nuiton.i18n.I18n.n; @@ -28,8 +49,6 @@ import org.nuiton.math.matrix.MatrixND; import org.nuiton.topia.TopiaException; -import static org.nuiton.i18n.I18n.n; - /** * * @author poussin @@ -498,9 +517,7 @@ * metier * * @param step - * @param matrixFishingMortality - * @param group - * @param zone + * @param matrixFishingMortalityPerCell * @return */ protected MatrixND totalFishingMortalityPerCell(TimeStep step, Added: trunk/sensitivityexports/SensitivityLbarJanvierY1.java =================================================================== --- trunk/sensitivityexports/SensitivityLbarJanvierY1.java (rev 0) +++ trunk/sensitivityexports/SensitivityLbarJanvierY1.java 2015-04-16 16:43:41 UTC (rev 352) @@ -0,0 +1,88 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2015 Ifremer, Code Lutin + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 2 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-2.0.html>. + * #L% + */ +package sensitivityexports; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixND; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.TimeStep; +import fr.ifremer.isisfish.util.Doc; + +public class SensitivityLbarJanvierY1 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(SensitivityLbarJanvierY1.class); + + protected String[] necessaryResult = { ResultName.MATRIX_LBAR }; + + @Doc("Population") + public Population param_pop; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + ResultStorage resultStorage = simulation.getResultStorage(); + TimeStep lastStep = resultStorage.getLastStep(); + TimeStep janvierLastYear = new TimeStep(12 * lastStep.getYear()); + double lbar = 0.0; + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + + //Get the lbar of the last time step + MatrixND matlastJan = resultStorage.getMatrix(janvierLastYear, pop, + ResultName.MATRIX_LBAR); + MatrixND meanLastJan = matlastJan.meanOverDim(0); // moyenne sur les zones + lbar = meanLastJan.sumAll(); // On somme tout mais en fait il n'y a plus qu'une valeur dans la matrice; permet d'avoir un double + } + } + out.write(Double.toString(lbar)); + } + + @Override + public String getDescription() { + return "lbar for January of the last year. lbar is the mean lbar over zones"; + } + + @Override + public String getExportFilename() { + return "SensitivityLbarJanvierY1_" + param_pop.getName(); + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} Property changes on: trunk/sensitivityexports/SensitivityLbarJanvierY1.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native Added: trunk/sensitivityexports/SensitivityRecruitmentY1.java =================================================================== --- trunk/sensitivityexports/SensitivityRecruitmentY1.java (rev 0) +++ trunk/sensitivityexports/SensitivityRecruitmentY1.java 2015-04-16 16:43:41 UTC (rev 352) @@ -0,0 +1,94 @@ +/* + * #%L + * IsisFish data + * %% + * Copyright (C) 2015 Ifremer, Code Lutin + * %% + * This program is free software: you can redistribute it and/or modify + * it under the terms of the GNU General Public License as + * published by the Free Software Foundation, either version 3 of the + * License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public + * License along with this program. If not, see + * <http://www.gnu.org/licenses/gpl-3.0.html>. + * #L% + */ +package sensitivityexports; + +import java.io.Writer; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixND; + +import scripts.ResultName; +import fr.ifremer.isisfish.datastore.ResultStorage; +import fr.ifremer.isisfish.datastore.SimulationStorage; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.export.SensitivityExport; +import fr.ifremer.isisfish.types.TimeStep; +import fr.ifremer.isisfish.util.Doc; + +public class SensitivityRecruitmentY1 implements SensitivityExport { + + /** to use log facility, just put in your code: log.info("..."); */ + static private Log log = LogFactory.getLog(SensitivityRecruitmentY1.class); + + protected String[] necessaryResult = { + ResultName.MATRIX_RECRUITMENT + }; + + @Doc("Population") + public Population param_pop; + + @Override + public void export(SimulationStorage simulation, Writer out) + throws Exception { + ResultStorage resultStorage = simulation.getResultStorage(); + TimeStep lastStep = resultStorage.getLastStep(); + double recruitment = 0.0; + + for (Population pop : simulation.getParameter().getPopulations()) { + if (pop.getName().equals(param_pop.getName())) { + for (int i = 0; i < 12; i++) { + + //Get the recruitment of each month of the last year + MatrixND matlastdate = resultStorage.getMatrix( + new TimeStep(lastStep.getStep() - i), + pop, + ResultName.MATRIX_RECRUITMENT); + recruitment += matlastdate.sumAll(); + } + } + } + + out.write(Double.toString(recruitment)); + } + + @Override + public String getDescription() { + return "Total recruitment for the last year for the population."; + } + + @Override + public String getExportFilename() { + return "SensitivityRecruitmentY1_" + param_pop.getName(); + } + + @Override + public String getExtensionFilename() { + return ".csv"; + } + + @Override + public String[] getNecessaryResult() { + return this.necessaryResult; + } + +} Property changes on: trunk/sensitivityexports/SensitivityRecruitmentY1.java ___________________________________________________________________ Added: svn:eol-style + native Added: svn:keywords + Author Date Id Revision HeadURL Modified: trunk/simulators/DefaultSimulator.java =================================================================== --- trunk/simulators/DefaultSimulator.java 2014-12-22 10:19:18 UTC (rev 351) +++ trunk/simulators/DefaultSimulator.java 2015-04-16 16:43:41 UTC (rev 352) @@ -1,9 +1,8 @@ - /* * #%L * IsisFish data * %% - * Copyright (C) 2006 - 2014 Ifremer, Code Lutin, Cedric Pineau, Benjamin Poussin, Chatellier Eric + * Copyright (C) 2006 - 2015 Ifremer, Code Lutin, Cedric Pineau, Benjamin Poussin, Chatellier Eric * %% * This program is free software: you can redistribute it and/or modify * it under the terms of the GNU General Public License as @@ -457,6 +456,16 @@ resManager.addResult(step, pop, biomassBM); } + if (resManager.isEnabled(ResultName.MATRIX_LBAR)) { + MatrixND Lbar = siMatrix.Lbar(step, pop, N); + resManager.addResult(step, pop, Lbar); + } + + if (resManager.isEnabled(ResultName.MATRIX_RECRUITMENT)) { + MatrixND Recruitment = siMatrix.Recruitment(step, pop); + resManager.addResult(step, pop, Recruitment); + } + MatrixND abundance; // compute fishing matrix only if there are one or more strategy if (siMatrix.getStrategies(step).size() > 0) {

1 0

r351 - trunk/simulators
by bpoussin＠users.forge.codelutin.com Dec. 22, 2014

Dec. 22, 2014

Author: bpoussin Date: 2014-12-22 10:19:18 +0000 (Mon, 22 Dec 2014) New Revision: 351 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/351 Log: - remove dbResult transaction commit (no more needed with ResultStorageCSV) - change TimeStep before rollback to permit export of database Modified: trunk/simulators/DefaultSimulator.java Modified: trunk/simulators/DefaultSimulator.java =================================================================== --- trunk/simulators/DefaultSimulator.java 2014-12-18 12:20:31 UTC (rev 350) +++ trunk/simulators/DefaultSimulator.java 2014-12-22 10:19:18 UTC (rev 351) @@ -102,7 +102,7 @@ TimeStep step = control.getStep(); ResultManager resManager = context.getResultManager(); - TopiaContext db = context.getDB(); + TopiaContext db = context.getDB(); // for database init SiMatrix siMatrix = newSiMatrix(context); GravityModel gravityModel = newGravityModel(context, siMatrix); @@ -137,7 +137,7 @@ // // Commit all change done un init rules methods. // - context.getDB().commitTransaction(); + context.validateDBChanges(); // // Simulation loop @@ -174,9 +174,9 @@ if (siMatrix.getStrategies(step).size() > 0) { if (resManager.isEnabled(ResultName.MATRIX_NO_ACTIVITY)) { MatrixND mat = metierMonitor.getOrCreateNoActivity(step, - ResultName.MATRIX_NO_ACTIVITY, siMatrix + ResultName.MATRIX_NO_ACTIVITY, siMatrix .getStrategies(step), siMatrix - .getMetiers(step)); + .getMetiers(step)); resManager.addResult(step, mat); } } @@ -214,7 +214,7 @@ for (Rule rule : rules) { for (Metier metier : siMatrix.getMetiers(step)) { boolean condition = ruleMonitor.getEvalutionCondition(step, - rule, metier); + rule, metier); if (condition) { rule.preAction(context, step, metier); } @@ -343,22 +343,17 @@ } // - // revert modification for next step + // Go next step // - control.setText("Rollback rules changes"); - db.rollbackTransaction(); + // do next before rollbackTransaction to permit export to take + // current database value and export them. + step = step.next(); // - // commit result + // revert modification for next step // - control.setText("Commit results"); - TopiaContext tx = context.getDbResult(); - tx.commitTransaction(); - - // - // Go next step - // - step = step.next(); + control.setText("Rollback rules changes"); + context.rollbackRuleChanges(); } }

1 0

r350 - in trunk: scripts simulators
by bpoussin＠users.forge.codelutin.com Dec. 18, 2014

Dec. 18, 2014

Author: bpoussin Date: 2014-12-18 12:20:31 +0000 (Thu, 18 Dec 2014) New Revision: 350 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/350 Log: fixes #6322: Change DefaultSimulator, SiMatrix and GravityModel to permit easy overwrite method to create new simulator Added: trunk/scripts/SiMatrixEffortByCell.java Modified: trunk/scripts/SiMatrix.java trunk/simulators/DefaultSimulator.java trunk/simulators/SimulatorEffortByCell.java Modified: trunk/scripts/SiMatrix.java =================================================================== --- trunk/scripts/SiMatrix.java 2014-12-03 15:48:52 UTC (rev 349) +++ trunk/scripts/SiMatrix.java 2014-12-18 12:20:31 UTC (rev 350) @@ -79,9 +79,11 @@ protected SimulationContext context = null; protected TopiaContext db = null; + protected ResultManager resManager; /** - * Method used to get SiMatrix used for simulation + * Method used to get SiMatrix used for simulation, before call this method + * new SiMatrix must called * * @param context * context simulation @@ -91,9 +93,6 @@ public static SiMatrix getSiMatrix(SimulationContext context) throws TopiaException { SiMatrix result = (SiMatrix) context.getValue(SiMatrix.class.getName()); - if (result == null) { - result = new SiMatrix(context); - } return result; } @@ -110,10 +109,23 @@ public SiMatrix(SimulationContext context) throws TopiaException { this.context = context; this.db = context.getDB(); + this.resManager = context.getResultManager(); setSiMatrix(context, this); } /** + * This method permit to add some specific computation for specific Simulator. + * example use in SiMatrixEffortByCell + * + * @param step + * @param pop + * @param N + * @throws IsisFishException + */ + public void computeMonthExtra(TimeStep step, Population pop, MatrixND N) throws TopiaException, IsisFishException { + } + + /** * @return * @throws TopiaException */ @@ -244,107 +256,6 @@ // /////////////////////////////////////////////////////////////////////////// - public MatrixND matrixCatchWeightPerStrategyMetPerZoneMet(TimeStep step, - Population pop, MatrixND matrixCatchPerStrategyMetPerZoneMet) - throws TopiaException, IsisFishException { - - return matrixToWeightMatrix(step, 2, - ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_MET, - matrixCatchPerStrategyMetPerZoneMet); - -// List<PopulationGroup> groups = pop.getPopulationGroup(); -// -// MatrixND result = matrixCatchPerStrategyMetPerZoneMet.copy(); -// result.setName(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_MET); -// -// for (PopulationGroup group : groups) { -// MatrixND sub = result.getSubMatrix(2, group, 1); -// double meanWeight = group.getMeanWeight(); -// sub.mults(meanWeight); -// } -// -// return result; - } - - public MatrixND matrixCatchPerStrategyMetPerZoneMet(MatrixND N, - Population pop, TimeStep step) throws TopiaException, IsisFishException { - - MatrixND matrixFishingMortalityPerCell = matrixFishingMortalityPerCell( - step, pop); - MatrixND matrixCatchRatePerStrategyMetPerCell = matrixCatchRatePerStrategyMetPerCell( - pop, step, matrixFishingMortalityPerCell); - MatrixND matrixCatchPerStrategyMetPerCell = matrixCatchPerStrategyMetPerCell( - N, pop, step, matrixCatchRatePerStrategyMetPerCell); - - List<Strategy> strategies = getStrategies(step); - List<Metier> metiers = getMetiers(step); - List<PopulationGroup> groups = (List<PopulationGroup>)matrixCatchPerStrategyMetPerCell - .getSemantic(2); - List<Zone> zones = getZones(step); - - Set<Cell> cellPops = new HashSet(matrixCatchPerStrategyMetPerCell - .getSemantic(4)); - - MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_MET, - new List[] { strategies, metiers, groups, zones }, - new String[] { n("Strategies"), n("Metiers"), n("Groups"), - n("Zones") }); - - // matrice temporaire ou les zones pops sont sommees - MatrixND tmp = matrixCatchPerStrategyMetPerCell.sumOverDim(3); - tmp = tmp.reduceDims(3); - - for (int s = 0; s < strategies.size(); s++) { - Strategy str = strategies.get(s); - for (int g = 0; g < groups.size(); g++) { - PopulationGroup group = groups.get(g); - // on iter que sur les metiers qui ont une proportion non 0 - // car la matrice pour les autres metiers, contient 0. - List<Metier> metiersNot0 = getMetiers(str, step); - for (int m = 0; m < metiersNot0.size(); m++) { - Metier metier = metiersNot0.get(m); - MetierSeasonInfo infoMet = metier.getMetierSeasonInfo(step - .getMonth()); - Collection<Zone> zoneMet = infoMet.getZone(); - for (Zone z : zoneMet) { - double value = 0; - List<Cell> cells = z.getCell(); - for (int c = 0; c < cells.size(); c++) { - Cell cell = cells.get(c); - if (cellPops.contains(cell)) { - // les cells de la matrice sont les cells des - // zones pops, donc seul les intersections avec - // les cells des metiers sont des cells valides - value += tmp.getValue(str, metier, group, cell); - } - } - result.setValue(str, metier, group, z, value); - } - } - } - } - - return result; - } - - public MatrixND matrixCatchPerStrategyMetPerZonePop(MatrixND N, - Population pop, TimeStep step) throws TopiaException, IsisFishException { - MatrixND matrixFishingMortalityPerCell = matrixFishingMortalityPerCell( - step, pop); - MatrixND matrixCatchRatePerStrategyMetPerCell = matrixCatchRatePerStrategyMetPerCell( - pop, step, matrixFishingMortalityPerCell); - MatrixND matrixCatchPerStrategyMetPerCell = matrixCatchPerStrategyMetPerCell( - N, pop, step, matrixCatchRatePerStrategyMetPerCell); - - // on somme sur les cellules - MatrixND result = matrixCatchPerStrategyMetPerCell.sumOverDim(4); - result = result.reduceDims(4); - result.setName(ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP); - - return result; - } - public MatrixND matrixCatchWeightPerStrategyMetPerZonePop(TimeStep step, Population pop, MatrixND matrixCatchPerStrategyMetPerZonePop) throws TopiaException, IsisFishException { @@ -352,19 +263,6 @@ return matrixToWeightMatrix(step, 2, ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP, matrixCatchPerStrategyMetPerZonePop); - -// List<PopulationGroup> groups = pop.getPopulationGroup(); -// -// MatrixND result = matrixCatchPerStrategyMetPerZonePop.copy(); -// result.setName(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP); -// -// for (PopulationGroup group : groups) { -// MatrixND sub = result.getSubMatrix(2, group, 1); -// double meanWeight = group.getMeanWeight(); -// sub.mults(meanWeight); -// } -// -// return result; } /** @@ -381,9 +279,11 @@ * @throws IsisFishException */ public MatrixND matrixCatchPerStrategyMetPerZone(MatrixND N, - Population pop, TimeStep step, MatrixND matrixCatchRatePerStrategyMet) + Population pop, TimeStep step) throws TopiaException, IsisFishException { + MatrixND matrixCatchRatePerStrategyMet = matrixCatchRatePerStrategyMetPerZone(pop, step); + int dimGroup = 2; int dimZone = 3; @@ -398,21 +298,6 @@ } return result; -// List<PopulationGroup> groups = pop.getPopulationGroup(); -// List<Zone> zones = pop.getPopulationZone(); -// -// MatrixND result = matrixCatchRatePerStrategyMet.copy(); -// result.setName(ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP); -// -// for (PopulationGroup group : groups) { -// MatrixND sub = result.getSubMatrix(2, group, 1); -// for (Zone zone : zones) { -// MatrixND subsub = sub.getSubMatrix(3, zone, 1); -// double val = N.getValue(group, zone); -// subsub.mults(val); -// } -// } -// return result; } /** @@ -426,9 +311,11 @@ * @throws TopiaException * @throws IsisFishException */ - public MatrixND matrixCatchRatePerStrategyMetPerZone(Population pop, - TimeStep step, MatrixND matrixFishingMortality) throws TopiaException, + public MatrixND matrixCatchRatePerStrategyMetPerZone(Population pop, TimeStep step) throws TopiaException, IsisFishException { + + MatrixND matrixFishingMortality = matrixFishingMortality(step, pop); + List<Strategy> strategies = getStrategies(step); List<Metier> metiers = getMetiers(step); List<PopulationGroup> groups = pop.getPopulationGroup(); @@ -462,6 +349,7 @@ } } } + resManager.addResult(step, pop, result); return result; } @@ -490,8 +378,44 @@ return result; } + /** + * @param str + * @param metier + * @param step + * @return + */ + protected double effortPerStrategyPerCell(Strategy str, Metier metier, + MetierSeasonInfo infoMet, TimeStep step) { + //StrategyMonthInfo smi = str.getStrategyMonthInfo(month); + Collection<Zone> zones = infoMet.getZone(); + double nbCell = getCells(zones).size(); + + if (nbCell == 0) { + // normalement il devrait y avoir des mailles, mais pour les + // ancienne zone AuPort, il n'y en avait pas + if (log.isWarnEnabled()) { + Month month = step.getMonth(); + log.warn("Calcul d'une distance pour le metier " + metier + + " pour le mois " + month + + " avec une zone sans maille: " + zones); + } + return 0; + } + + double effortPerStrategy = effortPerStrategyMet(str, metier, step); + + if (log.isDebugEnabled()) { + log.debug(" strategy=" + str + " metier=" + metier + " nbCell=" + + nbCell + " effortPerStrategy=" + effortPerStrategy); + } + + double result = effortPerStrategy / nbCell; + + return result; + } + // Optimisation Hilaire - private double catchRatePerStrategyMet(Strategy str, Metier metier, + protected double catchRatePerStrategyMet(Strategy str, Metier metier, TimeStep step, PopulationGroup group, Zone zone, MatrixND matrixFishingMortality) throws TopiaException, IsisFishException { @@ -567,83 +491,6 @@ return result; } -// /** -// * Matrice fishing mortality dim [ Strategy x Metier x Classe x zonePop ] -// * -// * @param pop -// * @param step -// * @return -// * @throws TopiaException -// * @throws IsisFishException -// */ -// public MatrixND matrixFishingMortality(TimeStep step, Population pop) -// throws TopiaException, IsisFishException { -// List<Strategy> strategies = getStrategies(step); -// List<Metier> metiers = getMetiers(step); -// List<PopulationGroup> groups = pop.getPopulationGroup(); -// List<Zone> zones = pop.getPopulationZone(); -// -// // default value in matrix is 0 -// MatrixND result = MatrixFactory.getInstance().create( -// ResultName.MATRIX_FISHING_MORTALITY, -// new List[] { strategies, metiers, groups, zones }, -// new String[] { n("Strategies"), n("Metiers"), n("Groups"), -// n("Zones") }); -// -// Month month = step.getMonth(); -// PopulationSeasonInfo infoPop = pop.getPopulationSeasonInfo(month); -// -// for (int g = 0; g < groups.size(); g++) { -// PopulationGroup group = groups.get(g); -// -// // getCapturability is check matrix validity and create matrix if needed and get one value in -// double capturability = infoPop.getCapturability(group); -// if (capturability != 0) { // check 0, this prevent next call, for default value -// -// for (int m = 0; m < metiers.size(); m++) { -// Metier metier = metiers.get(m); -// -// MetierSeasonInfo infoMet = metier -// .getMetierSeasonInfo(month); -// // getTargetFactor seem to be simple -// double ciblage = infoMet.getTargetFactor(group); -// -// if (ciblage != 0) { // check 0, this prevent next call, for default value -// -// Gear gear = metier.getGear(); -// Selectivity selectivity = gear -// .getPopulationSelectivity(pop); -// if (selectivity != null) { -// -// // getCoefficient is equation evaluation -// double coeff = selectivity.getCoefficient(pop, -// group, metier); -// if (coeff != 0) { // check 0, this prevent next call, for default value -// -// for (int s = 0; s < strategies.size(); s++) { -// Strategy str = strategies.get(s); -// for (int z = 0; z < zones.size(); z++) { -// Zone zone = zones.get(z); -// double effort = effortPerZonePop(str, -// metier, infoMet, step, zone); -// if (effort > 0) { // put value only if <> 0 -// double value = coeff -// * capturability * ciblage -// * effort; -// result.setValue(str, metier, group, -// zone, value); -// } -// } -// } -// } -// } -// } -// } -// } -// } -// return result; -// } - /** * Matrice fishing mortality dim [ Strategy x Metier x Classe x zonePop ] * @@ -730,519 +577,16 @@ } } } + resManager.addResult(step, pop, result); return result; } - /** - * Matrice des captures en nombre dim [ Strategy x Metier x Classe x zonePop ] - * - * @param N - * l'abondance sous forme de matrice 2D [class x zone] - * @param pop - * @param step - * @return - * @throws TopiaException - * @throws IsisFishException - */ - private MatrixND matrixCatchPerStrategyMetPerCell(MatrixND N, - Population pop, TimeStep step, - MatrixND matrixCatchRatePerStrategyMetPerCell) - throws TopiaException, IsisFishException { - int groupDim = 2; - int zoneDim = 3; - - int NGroupDim = 0; - int NZoneDim = 1; - - MatrixND result = matrixCatchRatePerStrategyMetPerCell.copy(); - result.setName("matrixCatchPerStrategyMetPerCell"); - - List<PopulationGroup> groups = (List<PopulationGroup>)result.getSemantic(groupDim); - List<Zone> zones = (List<Zone>)result.getSemantic(zoneDim); - - double[] sizeCell = new double[zones.size()]; - int cpt = 0; - for (Zone z : zones) { - sizeCell[cpt++] = z.sizeCell(); - } - - // on suppose que les semantics de N et matrixCatchRatePerStrategyMetPerCell - // pour les PopulationGroup et Zone sont les memes - // mais on verifie tout de meme - if (groups.equals(N.getSemantic(NGroupDim)) && - zones.equals(N.getSemantic(NZoneDim))) { - - // on place les effectifs dans un tableau pour un acces rapide - // on divise directement par le nombre de cell de la zone pour eviter - // de le faire beaucoup plus souvent dans l'autre boucle - double[][] NArray = new double[groups.size()][zones.size()]; - for (MatrixIterator i=N.iteratorNotZero(); i.next();) { - int[] pos = i.getCoordinates(); - double val = i.getValue(); - - NArray[pos[NGroupDim]][pos[NZoneDim]] = val / sizeCell[pos[NZoneDim]]; - } - - // calcul de la matrice resultat - for (MatrixIterator i=result.iteratorNotZero(); i.next();) { - int[] pos = i.getCoordinates(); - double val = i.getValue(); - val *= NArray[pos[groupDim]][pos[zoneDim]]; - i.setValue(val); - } - - } else { - // N et matrixCatchRatePerStrategyMetPerCell non pas les meme semantics - // on fait moins rapide - for (MatrixIterator i=result.iteratorNotZero(); i.next();) { - int[] pos = i.getCoordinates(); - Object[] sems = i.getSemanticsCoordinates(); - PopulationGroup group = (PopulationGroup)sems[groupDim]; - Zone zone = (Zone)sems[zoneDim]; - double val = i.getValue(); - val *= N.getValue(group, zone) / sizeCell[pos[zoneDim]]; - i.setValue(val); - } - } - - return result; - -// List<PopulationGroup> groups = pop.getPopulationGroup(); -// List<Zone> zones = pop.getPopulationZone(); -// -// MatrixND result = matrixCatchRatePerStrategyMetPerCell.copy(); -// result.setName("matrixCatchPerStrategyMetPerCell"); -// -// for (PopulationGroup group : groups) { -// MatrixND sub = result.getSubMatrix(2, group, 1); -// for (Zone zone : zones) { -// MatrixND subsub = sub.getSubMatrix(3, zone, 1); -// double val = N.getValue(group, zone) / (double) zone.sizeCell(); -// subsub.mults(val); -// } -// } -// return result; - } - - /** - * Matrice des captures en poids dim [ Strategy x Metier x Classe x zonePop ] - * - * @param pop - * @param step - * @return - * @throws TopiaException - * @throws IsisFishException - */ - private MatrixND matrixCatchRatePerStrategyMetPerCell(Population pop, - TimeStep step, MatrixND matrixFishingMortalityPerCell) - throws TopiaException, IsisFishException { - - MatrixND totalFishingMortalityPerCell = totalFishingMortalityPerCell( - step, matrixFishingMortalityPerCell); - - MatrixND result = matrixFishingMortalityPerCell.copy(); - result.setName("matrixCatchRatePerStrategyMetPerCell"); - - for (MatrixIterator i=result.iteratorNotZero(); i.next();) { - Object[] sems = i.getSemanticsCoordinates(); - - PopulationGroup group = (PopulationGroup)sems[2]; - Zone zone = (Zone)sems[3]; - Cell cell = (Cell)sems[4]; - - double totalFishingMortality = totalFishingMortalityPerCell.getValue( - group, zone, cell); - - if (totalFishingMortality != 0) { - - double fishingMortalityPerCell = i.getValue(); - double totalCatchRatePerCell = totalCatchRatePerCell(step, group, zone, - totalFishingMortality); - - double value = fishingMortalityPerCell / totalFishingMortality - * totalCatchRatePerCell; - - i.setValue(value); - } - } - - return result; - - -// List<Strategy> strategies = getStrategies(step); -// List<Metier> metiers = getMetiers(step); -// List<PopulationGroup> groups = pop.getPopulationGroup(); -// List<Zone> zones = pop.getPopulationZone(); -// List<Cell> cells = getCells(zones); -// -// MatrixND result = MatrixFactory.getInstance().create( -// "matrixCatchRatePerStrategyMetPerCell", -// new List[] { strategies, metiers, groups, zones, cells }, -// new String[] { n("Strategies"), n("Metiers"), n("Groups"), -// n("Zones"), n("Cells") }); -// -// // Optimisation Hilaire -// MatrixND matrixFishingMortalityPerCellSumOverGroup = matrixFishingMortalityPerCell -// .sumOverDim(2); -// matrixFishingMortalityPerCellSumOverGroup = matrixFishingMortalityPerCellSumOverGroup -// .reduceDims(2); -// -// for (int s = 0; s < strategies.size(); s++) { -// Strategy str = strategies.get(s); -// metiers = getMetiers(str, step); -// for (int m = 0; m < metiers.size(); m++) { -// Metier metier = metiers.get(m); -// for (int z = 0; z < zones.size(); z++) { -// Zone zone = zones.get(z); -// List<Cell> cellZones = zone.getCell(); -// for (int c = 0; c < cellZones.size(); c++) { -// Cell cell = cellZones.get(c); -// double effort = matrixFishingMortalityPerCellSumOverGroup -// .getValue(str, metier, zone, cell); -// if (effort > 0) { -// for (int g = 0; g < groups.size(); g++) { -// PopulationGroup group = groups.get(g); -// double value = catchRatePerStrategyMetPerCell( -// str, metier, step, group, zone, cell, -// matrixFishingMortalityPerCell); -// result.setValue(new Object[] { str, metier, -// group, zone, cell }, value); -// } -// } -// } -// } -// } -// } -// -// return result; - } -// directement dans matrixCatchRatePerStrategyMetPerCell pour pouvoir mieux optimiser -// /** -// * catchRatePerStrategyMetPerCell. -// * -// * Optimisation Hilaire -// * -// * @param str -// * @param metier -// * @param step -// * @param group -// * @param zone -// * @param cell -// * @param matrixFishingMortalityPerCell -// * @return -// * @throws TopiaException -// * @throws IsisFishException -// */ -// private double catchRatePerStrategyMetPerCell(Strategy str, Metier metier, -// TimeStep step, PopulationGroup group, Zone zone, Cell cell, -// MatrixND matrixFishingMortalityPerCell) throws TopiaException, -// IsisFishException { -// -// MatrixND totalFishingMortalityPerCell = totalFishingMortalityPerCell( -// step, matrixFishingMortalityPerCell); -// double totalFishingMortality = totalFishingMortalityPerCell.getValue( -// group, zone, cell); -// -// if (totalFishingMortality == 0) { -// if (log.isDebugEnabled()) { -// log.debug("pas de totalFishingMortality pour (" + group + ", " -// + zone + ")"); -// } -// return 0; -// } -// -// double fishingMortalityPerCell = matrixFishingMortalityPerCell -// .getValue(new Object[] { str, metier, group, zone, cell }); -// double totalCatchRatePerCell = totalCatchRatePerCell(step, group, zone, -// totalFishingMortality); -// -// if (log.isDebugEnabled()) { -// log.debug(" totalFishingMortality=" + totalFishingMortality -// + " fishingMortality=" + fishingMortalityPerCell -// + " totalCatchRate=" + totalCatchRatePerCell); -// } -// double result = fishingMortalityPerCell / totalFishingMortality -// * totalCatchRatePerCell; -// -// return result; -// } - - /** - * @param step - * @param group - * @param zone - * @param totalFishingMortality - * @return - * @throws TopiaException - */ - private double totalCatchRatePerCell(TimeStep step, PopulationGroup group, - Zone zone, double totalFishingMortalityPerCell) - throws TopiaException { - double M = group.getNaturalDeathRate(zone) / Month.NUMBER_OF_MONTH; - if (M == 0) { - // normalement il devrait y avoir de la mortalite naturelle - if (log.isWarnEnabled()) { - log.warn("Pas de mortalite naturelle pour: " + group); - } - } - double F = totalFishingMortalityPerCell; - - double result = 0; - if (M != 0 || F != 0) { - result = F / (F + M) * (1 - Math.exp(-(F + M))); - } - - return result; - } - - /** - * Returne une matrice de mortalite group x zone, donc somme sur str et - * metier - * - * @param step - * @param matrixFishingMortality - * @param group - * @param zone - * @return - */ - private MatrixND totalFishingMortalityPerCell(TimeStep step, - MatrixND matrixFishingMortalityPerCell) { - MatrixND result = matrixFishingMortalityPerCell.sumOverDim(0); - result = result.sumOverDim(1); - result = result.reduceDims(0, 1); - return result; - } - -// /** -// * Matrice fishing mortality dim [ Strategy x Metier x Classe x zonePop x -// * cellPop] -// * -// * Nouvelle implantation suite a demande Steph et Sigrid: 20080208 (NouvellesEquationsfev2008ParCelluleAvecAlgo.odt) -// * -// * @param pop -// * @param step -// * @return -// * @throws TopiaException -// * @throws IsisFishException -// */ -// public MatrixND matrixFishingMortalityPerCell(TimeStep step, Population pop) -// throws TopiaException, IsisFishException { -// List<Strategy> strategies = getStrategies(step); -// List<Metier> metiers = getMetiers(step); -// List<PopulationGroup> groups = pop.getPopulationGroup(); -// List<Zone> zones = pop.getPopulationZone(); -// List<Cell> cells = getCells(zones); -// -// // default value in matrix is 0 -// MatrixND result = MatrixFactory.getInstance().create( -// "matrixFishingMortalityPerCell", -// new List[] { strategies, metiers, groups, zones, cells }, -// new String[] { n("Strategies"), n("Metiers"), n("Groups"), -// n("Zones"), n("Cells") }); -// -// Month month = step.getMonth(); -// PopulationSeasonInfo infoPop = pop.getPopulationSeasonInfo(month); -// -// for (int g = 0; g < groups.size(); g++) { -// PopulationGroup group = groups.get(g); -// -// // getCapturability is check matrix validity and create matrix -// // if needed and get one value in -// double capturability = infoPop.getCapturability(group); -// if (capturability != 0) { // check 0, this prevent next call, for default value -// for (int m = 0; m < metiers.size(); m++) { -// Metier metier = metiers.get(m); -// -// MetierSeasonInfo infoMet = metier -// .getMetierSeasonInfo(month); -// // getTargetFactor seem to be simple -// double ciblage = infoMet.getTargetFactor(group); -// -// if (ciblage != 0) { // check 0, this prevent next call, for default value -// -// Gear gear = metier.getGear(); -// Selectivity selectivity = gear.getPopulationSelectivity(pop); -// if (selectivity != null) { -// -// // getCoefficient is equation evaluation -// double coeff = selectivity.getCoefficient(pop,group, metier); -// if (coeff != 0) { // check 0, this prevent next call, for default value -// -// for (int s = 0; s < strategies.size(); s++) { -// Strategy str = strategies.get(s); -// // l'effort d'une cellule du metier -// double effort = effortPerStrategyPerCell( -// str, metier, infoMet, step); -// if (effort > 0) { // put value only if <> 0 -// for (int z = 0; z < zones.size(); z++) { -// Zone zone = zones.get(z); -// Set<Cell> cellPops = new HashSet<Cell>(zone.getCell()); -// for (Cell cellMet : infoMet.getCells()) { -// if (cellPops.contains(cellMet)) { -// double value = coeff * capturability * ciblage * effort; -// result.setValue( -// new Object[] { str, -// metier, -// group, -// zone, -// cellMet }, -// value); -// } -// } -// } -// } -// } -// } -// } -// } -// } -// } -// } -// return result; -// } -// - - /** - * Matrice fishing mortality dim [ Strategy x Metier x Classe x zonePop x - * cellPop] - * - * Nouvelle implantation suite a demande Steph et Sigrid: 20080208 (NouvellesEquationsfev2008ParCelluleAvecAlgo.odt) - * - * @param pop - * @param step - * @return - * @throws TopiaException - * @throws IsisFishException - */ - public MatrixND matrixFishingMortalityPerCell(TimeStep step, Population pop) - throws TopiaException, IsisFishException { - List<Strategy> strategies = getStrategies(step); - List<Metier> metiers = getMetiers(step); - List<PopulationGroup> groups = pop.getPopulationGroup(); - List<Zone> zones = pop.getPopulationZone(); - List<Cell> cells = getCells(zones); - - // default value in matrix is 0 - MatrixND result = MatrixFactory.getInstance().create( - "matrixFishingMortalityPerCell", - new List[] { strategies, metiers, groups, zones, cells }, - new String[] { n("Strategies"), n("Metiers"), n("Groups"), - n("Zones"), n("Cells") }); - - Month month = step.getMonth(); - PopulationSeasonInfo infoPop = pop.getPopulationSeasonInfo(month); - - for (Strategy str : strategies) { - StrategyMonthInfo smi = str.getStrategyMonthInfo(month); - double nbTrip = smi.getNumberOfTrips(); - double propSetOfVessels = str.getProportionSetOfVessels(); - int nbOfVessels = str.getSetOfVessels().getNumberOfVessels(); - - // dans le calcul de l'effort si une de ces donnees est 0 - // alors le result dans la matrice est 0 - // donc autant ne pas faire tous les autres calculs couteux - if (nbTrip * propSetOfVessels * nbOfVessels != 0) { - for (PopulationGroup group : groups) { - - // getCapturability is check matrix validity and create matrix if needed and get one value in - double capturability = infoPop.getCapturability(group); - if (capturability != 0) { // check 0, this prevent next call, for default value - - // et de la meme facon si la proportion est 0 alors - // le resultat dans la matrice sera 0, donc on boucle que - // sur ceux qui ont une proportion - List<Metier> metiersNot0 = getMetiers(str, step); - for (Metier metier : metiersNot0) { - - MetierSeasonInfo infoMet = metier - .getMetierSeasonInfo(month); - // getTargetFactor seem to be simple - double ciblage = infoMet.getTargetFactor(group); - - if (ciblage != 0) { // check 0, this prevent next call, for default value - - Gear gear = metier.getGear(); - Selectivity selectivity = gear.getPopulationSelectivity(pop); - if (selectivity != null) { - - // getCoefficient is equation evaluation - double coeff = selectivity.getCoefficient(pop,group, metier); - if (coeff != 0) { // check 0, this prevent next call, for default value - - // l'effort d'une cellule du metier - double effort = effortPerStrategyPerCell( - str, metier, infoMet, step); - if (effort > 0) { // put value only if <> 0 - for (Zone zone : zones) { - Set<Cell> cellPops = new HashSet<Cell>(zone.getCell()); - for (Cell cellMet : infoMet.getCells()) { - if (cellPops.contains(cellMet)) { - double value = coeff * capturability * ciblage * effort; - result.setValue( - new Object[] { str, - metier, - group, - zone, - cellMet }, - value); - } - } - } - } - } - } - } - } - } - } - } - } - return result; - } - - /** * @param str * @param metier * @param step * @return */ - private double effortPerStrategyPerCell(Strategy str, Metier metier, - MetierSeasonInfo infoMet, TimeStep step) { - //StrategyMonthInfo smi = str.getStrategyMonthInfo(month); - Collection<Zone> zones = infoMet.getZone(); - double nbCell = getCells(zones).size(); - - if (nbCell == 0) { - // normalement il devrait y avoir des mailles, mais pour les - // ancienne zone AuPort, il n'y en avait pas - if (log.isWarnEnabled()) { - Month month = step.getMonth(); - log.warn("Calcul d'une distance pour le metier " + metier - + " pour le mois " + month - + " avec une zone sans maille: " + zones); - } - return 0; - } - - double effortPerStrategy = effortPerStrategyMet(str, metier, step); - - if (log.isDebugEnabled()) { - log.debug(" strategy=" + str + " metier=" + metier + " nbCell=" - + nbCell + " effortPerStrategy=" + effortPerStrategy); - } - - double result = effortPerStrategy / nbCell; - - return result; - } - - /** - * @param str - * @param metier - * @param step - * @return - */ private double effortNominalPerStrategyMet(Strategy str, Metier metier, TimeStep step) { Month month = step.getMonth(); StrategyMonthInfo smi = str.getStrategyMonthInfo(month); @@ -1303,7 +647,7 @@ * @param step * @return */ - private double effortPerStrategyMet(Strategy str, Metier metier, TimeStep step) { + protected double effortPerStrategyMet(Strategy str, Metier metier, TimeStep step) { Month month = step.getMonth(); StrategyMonthInfo smi = str.getStrategyMonthInfo(month); @@ -1545,71 +889,6 @@ /////////////////////////////////////////////////////////////////////////// /** - * @param N - * @param pop - * @param step - * @return - * @throws IsisFishException - * @throws TopiaException - */ - private MatrixND matrixAbundancePerCell(MatrixND N, Population pop, - TimeStep step, MatrixND matrixFishingMortality) throws TopiaException, - IsisFishException { - - List<PopulationGroup> groups = pop.getPopulationGroup(); - List<Zone> zones = pop.getPopulationZone(); - List<Cell> allCells = getCells(zones); - - MatrixND result = MatrixFactory.getInstance().create( - ResultName.MATRIX_ABUNDANCE + "_PER_CELL", - new List[] { groups, zones, allCells }, - new String[] { n("Groups"), n("Zones"), n("Cells") }); - - for (int g = 0; g < groups.size(); g++) { - PopulationGroup group = groups.get(g); - for (int z = 0; z < zones.size(); z++) { - Zone zone = zones.get(z); - List<Cell> cells = zone.getCell(); - for (int c = 0; c < cells.size(); c++) { - Cell cell = cells.get(c); - double value = survivalRatePerCell(step, group, zone, cell, - matrixFishingMortality); - double n = N.getValue(g, z) / zone.sizeCell(); - value *= n; - result.setValue(g, z, c, value); - } - } - } - - return result; - } - - /** - * Utilise pour le calcule en Cell. - * - * @param N - * @param pop - * @param step - * @return - * @throws IsisFishException - * @throws TopiaException - */ - public MatrixND matrixAbundance(MatrixND N, Population pop, TimeStep step) - throws TopiaException, IsisFishException { - - MatrixND matrixFishingMortalityPerCell = matrixFishingMortalityPerCell( - step, pop); - - MatrixND result = matrixAbundancePerCell(N, pop, step, - matrixFishingMortalityPerCell); - result = result.sumOverDim(2); - result = result.reduceDims(2); - result.setName(ResultName.MATRIX_ABUNDANCE); - - return result; - } - - /** * Utilise pour le calcule en Zone. * * @param N @@ -1620,9 +899,11 @@ * @throws IsisFishException * @throws TopiaException */ - public MatrixND matrixAbundance(MatrixND N, Population pop, TimeStep step, - MatrixND matrixFishingMortality) throws TopiaException, + public MatrixND matrixAbundance(MatrixND N, Population pop, TimeStep step) throws TopiaException, IsisFishException { + + MatrixND matrixFishingMortality = matrixFishingMortality(step, pop); + List<PopulationGroup> groups = pop.getPopulationGroup(); List<Zone> zones = pop.getPopulationZone(); @@ -1690,7 +971,7 @@ * @throws IsisFishException * @throws TopiaException */ - private double survivalRatePerZone(TimeStep step, PopulationGroup group, + protected double survivalRatePerZone(TimeStep step, PopulationGroup group, Zone zone, MatrixND matrixFishingMortality) throws TopiaException, IsisFishException { double F = totalFishingMortality(step, matrixFishingMortality) @@ -1702,27 +983,6 @@ return result; } - /** - * @param step - * @param group - * @param zone - * @return - * @throws IsisFishException - * @throws TopiaException - */ - private double survivalRatePerCell(TimeStep step, PopulationGroup group, - Zone zone, Cell cell, MatrixND matrixFishingMortalityPerCell) - throws TopiaException, IsisFishException { - - double F = totalFishingMortalityPerCell(step, - matrixFishingMortalityPerCell).getValue(group, zone, cell); //totalFishingMortality(step, group, zone); // rem perf: totalFishingMortality a deja ete calcule - double M = group.getNaturalDeathRate(zone) - / (double) Month.NUMBER_OF_MONTH; - double result = (double) Math.exp(-(F + M)); - - return result; - } - /////////////////////////////////////////////////////////////////////////// // // Added: trunk/scripts/SiMatrixEffortByCell.java =================================================================== --- trunk/scripts/SiMatrixEffortByCell.java (rev 0) +++ trunk/scripts/SiMatrixEffortByCell.java 2014-12-18 12:20:31 UTC (rev 350) @@ -0,0 +1,514 @@ +package scripts; + +import static org.nuiton.i18n.I18n.n; + +import fr.ifremer.isisfish.IsisFishException; +import fr.ifremer.isisfish.entities.Cell; +import fr.ifremer.isisfish.entities.Gear; +import fr.ifremer.isisfish.entities.Metier; +import fr.ifremer.isisfish.entities.MetierSeasonInfo; +import fr.ifremer.isisfish.entities.Population; +import fr.ifremer.isisfish.entities.PopulationGroup; +import fr.ifremer.isisfish.entities.PopulationSeasonInfo; +import fr.ifremer.isisfish.entities.Selectivity; +import fr.ifremer.isisfish.entities.Strategy; +import fr.ifremer.isisfish.entities.StrategyMonthInfo; +import fr.ifremer.isisfish.entities.Zone; +import fr.ifremer.isisfish.simulator.SimulationContext; +import fr.ifremer.isisfish.types.Month; +import fr.ifremer.isisfish.types.TimeStep; +import java.util.Collection; +import java.util.HashSet; +import java.util.List; +import java.util.Set; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; +import org.nuiton.math.matrix.MatrixFactory; +import org.nuiton.math.matrix.MatrixIterator; +import org.nuiton.math.matrix.MatrixND; +import org.nuiton.topia.TopiaException; + +import static org.nuiton.i18n.I18n.n; + +/** + * + * @author poussin + * @version $Revision$ + * + * Last update: $Date$ + * by : $Author$ + */ +public class SiMatrixEffortByCell extends SiMatrix { + + /** to use log facility, just put in your code: log.info(\"...\"); */ + static private Log log = LogFactory.getLog(SiMatrixEffortByCell.class); + + public SiMatrixEffortByCell(SimulationContext context) throws TopiaException { + super(context); + } + + @Override + public void computeMonthExtra(TimeStep step, Population pop, MatrixND N) throws TopiaException, IsisFishException { + MatrixND catchPerStrategyMetPerZoneMet = + matrixCatchPerStrategyMetPerZoneMet(N, pop, step); + resManager.addResult(step, pop, catchPerStrategyMetPerZoneMet); + + if (resManager + .isEnabled(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_MET)) { + MatrixND catchWeightPerStrategyMet = + matrixCatchWeightPerStrategyMetPerZoneMet(step, + pop, catchPerStrategyMetPerZoneMet); + resManager.addResult(step, pop, catchWeightPerStrategyMet); + } + } + + protected MatrixND matrixCatchWeightPerStrategyMetPerZoneMet(TimeStep step, + Population pop, MatrixND matrixCatchPerStrategyMetPerZoneMet) + throws TopiaException, IsisFishException { + + return matrixToWeightMatrix(step, 2, + ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_MET, + matrixCatchPerStrategyMetPerZoneMet); + } + + protected MatrixND matrixCatchPerStrategyMetPerZoneMet(MatrixND N, + Population pop, TimeStep step) throws TopiaException, IsisFishException { + + MatrixND matrixFishingMortalityPerCell = matrixFishingMortalityPerCell( + step, pop); + MatrixND matrixCatchRatePerStrategyMetPerCell = matrixCatchRatePerStrategyMetPerCell( + pop, step, matrixFishingMortalityPerCell); + MatrixND matrixCatchPerStrategyMetPerCell = matrixCatchPerStrategyMetPerCell( + N, pop, step, matrixCatchRatePerStrategyMetPerCell); + + List<Strategy> strategies = getStrategies(step); + List<Metier> metiers = getMetiers(step); + List<PopulationGroup> groups = (List<PopulationGroup>)matrixCatchPerStrategyMetPerCell + .getSemantic(2); + List<Zone> zones = getZones(step); + + Set<Cell> cellPops = new HashSet(matrixCatchPerStrategyMetPerCell + .getSemantic(4)); + + MatrixND result = MatrixFactory.getInstance().create( + ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_MET, + new List[] { strategies, metiers, groups, zones }, + new String[] { n("Strategies"), n("Metiers"), n("Groups"), + n("Zones") }); + + // matrice temporaire ou les zones pops sont sommees + MatrixND tmp = matrixCatchPerStrategyMetPerCell.sumOverDim(3); + tmp = tmp.reduceDims(3); + + for (int s = 0; s < strategies.size(); s++) { + Strategy str = strategies.get(s); + for (int g = 0; g < groups.size(); g++) { + PopulationGroup group = groups.get(g); + // on iter que sur les metiers qui ont une proportion non 0 + // car la matrice pour les autres metiers, contient 0. + List<Metier> metiersNot0 = getMetiers(str, step); + for (int m = 0; m < metiersNot0.size(); m++) { + Metier metier = metiersNot0.get(m); + MetierSeasonInfo infoMet = metier.getMetierSeasonInfo(step + .getMonth()); + Collection<Zone> zoneMet = infoMet.getZone(); + for (Zone z : zoneMet) { + double value = 0; + List<Cell> cells = z.getCell(); + for (int c = 0; c < cells.size(); c++) { + Cell cell = cells.get(c); + if (cellPops.contains(cell)) { + // les cells de la matrice sont les cells des + // zones pops, donc seul les intersections avec + // les cells des metiers sont des cells valides + value += tmp.getValue(str, metier, group, cell); + } + } + result.setValue(str, metier, group, z, value); + } + } + } + } + + return result; + } + + + @Override + public MatrixND matrixCatchPerStrategyMetPerZone(MatrixND N, + Population pop, TimeStep step) throws TopiaException, IsisFishException { + MatrixND matrixFishingMortalityPerCell = matrixFishingMortalityPerCell( + step, pop); + MatrixND matrixCatchRatePerStrategyMetPerCell = matrixCatchRatePerStrategyMetPerCell( + pop, step, matrixFishingMortalityPerCell); + MatrixND matrixCatchPerStrategyMetPerCell = matrixCatchPerStrategyMetPerCell( + N, pop, step, matrixCatchRatePerStrategyMetPerCell); + + // on somme sur les cellules + MatrixND result = matrixCatchPerStrategyMetPerCell.sumOverDim(4); + result = result.reduceDims(4); + result.setName(ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP); + + return result; + } + + + /** + * Utilise pour le calcule en Cell. + * + * @param N + * @param pop + * @param step + * @return + * @throws IsisFishException + * @throws TopiaException + */ + @Override + public MatrixND matrixAbundance(MatrixND N, Population pop, TimeStep step) + throws TopiaException, IsisFishException { + + MatrixND matrixFishingMortalityPerCell = matrixFishingMortalityPerCell( + step, pop); + + MatrixND result = matrixAbundancePerCell(N, pop, step, + matrixFishingMortalityPerCell); + result = result.sumOverDim(2); + result = result.reduceDims(2); + result.setName(ResultName.MATRIX_ABUNDANCE); + + return result; + } + + /** + * @param N + * @param pop + * @param step + * @return + * @throws IsisFishException + * @throws TopiaException + */ + protected MatrixND matrixAbundancePerCell(MatrixND N, Population pop, + TimeStep step, MatrixND matrixFishingMortality) throws TopiaException, + IsisFishException { + + List<PopulationGroup> groups = pop.getPopulationGroup(); + List<Zone> zones = pop.getPopulationZone(); + List<Cell> allCells = getCells(zones); + + MatrixND result = MatrixFactory.getInstance().create( + ResultName.MATRIX_ABUNDANCE + "_PER_CELL", + new List[] { groups, zones, allCells }, + new String[] { n("Groups"), n("Zones"), n("Cells") }); + + for (int g = 0; g < groups.size(); g++) { + PopulationGroup group = groups.get(g); + for (int z = 0; z < zones.size(); z++) { + Zone zone = zones.get(z); + List<Cell> cells = zone.getCell(); + for (int c = 0; c < cells.size(); c++) { + Cell cell = cells.get(c); + double value = survivalRatePerCell(step, group, zone, cell, + matrixFishingMortality); + double n = N.getValue(g, z) / zone.sizeCell(); + value *= n; + result.setValue(g, z, c, value); + } + } + } + + return result; + } + + /** + * @param step + * @param group + * @param zone + * @return + * @throws IsisFishException + * @throws TopiaException + */ + protected double survivalRatePerCell(TimeStep step, PopulationGroup group, + Zone zone, Cell cell, MatrixND matrixFishingMortalityPerCell) + throws TopiaException, IsisFishException { + + double F = totalFishingMortalityPerCell(step, + matrixFishingMortalityPerCell).getValue(group, zone, cell); //totalFishingMortality(step, group, zone); // rem perf: totalFishingMortality a deja ete calcule + double M = group.getNaturalDeathRate(zone) + / (double) Month.NUMBER_OF_MONTH; + double result = (double) Math.exp(-(F + M)); + + return result; + } + + /** + * Matrice fishing mortality dim [ Strategy x Metier x Classe x zonePop x + * cellPop] + * + * Nouvelle implantation suite a demande Steph et Sigrid: 20080208 (NouvellesEquationsfev2008ParCelluleAvecAlgo.odt) + * + * @param pop + * @param step + * @return + * @throws TopiaException + * @throws IsisFishException + */ + protected MatrixND matrixFishingMortalityPerCell(TimeStep step, Population pop) + throws TopiaException, IsisFishException { + List<Strategy> strategies = getStrategies(step); + List<Metier> metiers = getMetiers(step); + List<PopulationGroup> groups = pop.getPopulationGroup(); + List<Zone> zones = pop.getPopulationZone(); + List<Cell> cells = getCells(zones); + + // default value in matrix is 0 + MatrixND result = MatrixFactory.getInstance().create( + "matrixFishingMortalityPerCell", + new List[] { strategies, metiers, groups, zones, cells }, + new String[] { n("Strategies"), n("Metiers"), n("Groups"), + n("Zones"), n("Cells") }); + + Month month = step.getMonth(); + PopulationSeasonInfo infoPop = pop.getPopulationSeasonInfo(month); + + for (Strategy str : strategies) { + StrategyMonthInfo smi = str.getStrategyMonthInfo(month); + double nbTrip = smi.getNumberOfTrips(); + double propSetOfVessels = str.getProportionSetOfVessels(); + int nbOfVessels = str.getSetOfVessels().getNumberOfVessels(); + + // dans le calcul de l'effort si une de ces donnees est 0 + // alors le result dans la matrice est 0 + // donc autant ne pas faire tous les autres calculs couteux + if (nbTrip * propSetOfVessels * nbOfVessels != 0) { + for (PopulationGroup group : groups) { + + // getCapturability is check matrix validity and create matrix if needed and get one value in + double capturability = infoPop.getCapturability(group); + if (capturability != 0) { // check 0, this prevent next call, for default value + + // et de la meme facon si la proportion est 0 alors + // le resultat dans la matrice sera 0, donc on boucle que + // sur ceux qui ont une proportion + List<Metier> metiersNot0 = getMetiers(str, step); + for (Metier metier : metiersNot0) { + + MetierSeasonInfo infoMet = metier + .getMetierSeasonInfo(month); + // getTargetFactor seem to be simple + double ciblage = infoMet.getTargetFactor(group); + + if (ciblage != 0) { // check 0, this prevent next call, for default value + + Gear gear = metier.getGear(); + Selectivity selectivity = gear.getPopulationSelectivity(pop); + if (selectivity != null) { + + // getCoefficient is equation evaluation + double coeff = selectivity.getCoefficient(pop,group, metier); + if (coeff != 0) { // check 0, this prevent next call, for default value + + // l'effort d'une cellule du metier + double effort = effortPerStrategyPerCell( + str, metier, infoMet, step); + if (effort > 0) { // put value only if <> 0 + for (Zone zone : zones) { + Set<Cell> cellPops = new HashSet<Cell>(zone.getCell()); + for (Cell cellMet : infoMet.getCells()) { + if (cellPops.contains(cellMet)) { + // Reduction d'effort (generic): + double effortReduction = getEffortReduction(step, gear, cellMet); + + double value = (1.0 - effortReduction) * coeff * capturability * ciblage * effort; + result.setValue( + new Object[] { str, + metier, + group, + zone, + cellMet }, + value); + } + } + } + } + } + } + } + } + } + } + } + } + return result; + } + + protected double getEffortReduction(TimeStep step, Gear gear, Cell cellMet) { + return 0.0; + } + + /** + * Matrice des captures en nombre dim [ Strategy x Metier x Classe x zonePop ] + * + * @param N + * l'abondance sous forme de matrice 2D [class x zone] + * @param pop + * @param step + * @return + * @throws TopiaException + * @throws IsisFishException + */ + protected MatrixND matrixCatchPerStrategyMetPerCell(MatrixND N, + Population pop, TimeStep step, + MatrixND matrixCatchRatePerStrategyMetPerCell) + throws TopiaException, IsisFishException { + int groupDim = 2; + int zoneDim = 3; + + int NGroupDim = 0; + int NZoneDim = 1; + + MatrixND result = matrixCatchRatePerStrategyMetPerCell.copy(); + result.setName("matrixCatchPerStrategyMetPerCell"); + + List<PopulationGroup> groups = (List<PopulationGroup>)result.getSemantic(groupDim); + List<Zone> zones = (List<Zone>)result.getSemantic(zoneDim); + + double[] sizeCell = new double[zones.size()]; + int cpt = 0; + for (Zone z : zones) { + sizeCell[cpt++] = z.sizeCell(); + } + + // on suppose que les semantics de N et matrixCatchRatePerStrategyMetPerCell + // pour les PopulationGroup et Zone sont les memes + // mais on verifie tout de meme + if (groups.equals(N.getSemantic(NGroupDim)) && + zones.equals(N.getSemantic(NZoneDim))) { + + // on place les effectifs dans un tableau pour un acces rapide + // on divise directement par le nombre de cell de la zone pour eviter + // de le faire beaucoup plus souvent dans l'autre boucle + double[][] NArray = new double[groups.size()][zones.size()]; + for (MatrixIterator i=N.iteratorNotZero(); i.next();) { + int[] pos = i.getCoordinates(); + double val = i.getValue(); + + NArray[pos[NGroupDim]][pos[NZoneDim]] = val / sizeCell[pos[NZoneDim]]; + } + + // calcul de la matrice resultat + for (MatrixIterator i=result.iteratorNotZero(); i.next();) { + int[] pos = i.getCoordinates(); + double val = i.getValue(); + val *= NArray[pos[groupDim]][pos[zoneDim]]; + i.setValue(val); + } + + } else { + // N et matrixCatchRatePerStrategyMetPerCell non pas les meme semantics + // on fait moins rapide + for (MatrixIterator i=result.iteratorNotZero(); i.next();) { + int[] pos = i.getCoordinates(); + Object[] sems = i.getSemanticsCoordinates(); + PopulationGroup group = (PopulationGroup)sems[groupDim]; + Zone zone = (Zone)sems[zoneDim]; + double val = i.getValue(); + val *= N.getValue(group, zone) / sizeCell[pos[zoneDim]]; + i.setValue(val); + } + } + + return result; + } + + /** + * Matrice des captures en poids dim [ Strategy x Metier x Classe x zonePop ] + * + * @param pop + * @param step + * @return + * @throws TopiaException + * @throws IsisFishException + */ + protected MatrixND matrixCatchRatePerStrategyMetPerCell(Population pop, + TimeStep step, MatrixND matrixFishingMortalityPerCell) + throws TopiaException, IsisFishException { + + MatrixND totalFishingMortalityPerCell = totalFishingMortalityPerCell( + step, matrixFishingMortalityPerCell); + + MatrixND result = matrixFishingMortalityPerCell.copy(); + result.setName("matrixCatchRatePerStrategyMetPerCell"); + + for (MatrixIterator i=result.iteratorNotZero(); i.next();) { + Object[] sems = i.getSemanticsCoordinates(); + + PopulationGroup group = (PopulationGroup)sems[2]; + Zone zone = (Zone)sems[3]; + Cell cell = (Cell)sems[4]; + + double totalFishingMortality = totalFishingMortalityPerCell.getValue( + group, zone, cell); + + if (totalFishingMortality != 0) { + + double fishingMortalityPerCell = i.getValue(); + double totalCatchRatePerCell = totalCatchRatePerCell(step, group, zone, + totalFishingMortality); + + double value = fishingMortalityPerCell / totalFishingMortality + * totalCatchRatePerCell; + + i.setValue(value); + } + } + + return result; + } + + /** + * @param step + * @param group + * @param zone + * @param totalFishingMortality + * @return + * @throws TopiaException + */ + private double totalCatchRatePerCell(TimeStep step, PopulationGroup group, + Zone zone, double totalFishingMortalityPerCell) + throws TopiaException { + double M = group.getNaturalDeathRate(zone) / Month.NUMBER_OF_MONTH; + if (M == 0) { + // normalement il devrait y avoir de la mortalite naturelle + if (log.isWarnEnabled()) { + log.warn("Pas de mortalite naturelle pour: " + group); + } + } + double F = totalFishingMortalityPerCell; + + double result = 0; + if (M != 0 || F != 0) { + result = F / (F + M) * (1 - Math.exp(-(F + M))); + } + + return result; + } + + /** + * Returne une matrice de mortalite group x zone, donc somme sur str et + * metier + * + * @param step + * @param matrixFishingMortality + * @param group + * @param zone + * @return + */ + protected MatrixND totalFishingMortalityPerCell(TimeStep step, + MatrixND matrixFishingMortalityPerCell) { + MatrixND result = matrixFishingMortalityPerCell.sumOverDim(0); + result = result.sumOverDim(1); + result = result.reduceDims(0, 1); + return result; + } + +} Property changes on: trunk/scripts/SiMatrixEffortByCell.java ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Modified: trunk/simulators/DefaultSimulator.java =================================================================== --- trunk/simulators/DefaultSimulator.java 2014-12-03 15:48:52 UTC (rev 349) +++ trunk/simulators/DefaultSimulator.java 2014-12-18 12:20:31 UTC (rev 350) @@ -22,8 +22,8 @@ */ package simulators; -import fr.ifremer.isisfish.IsisFish; import fr.ifremer.isisfish.IsisFishException; +import fr.ifremer.isisfish.datastore.StorageException; import fr.ifremer.isisfish.entities.Metier; import fr.ifremer.isisfish.entities.Population; import fr.ifremer.isisfish.entities.PopulationSeasonInfo; @@ -70,6 +70,27 @@ static private Log log = LogFactory.getLog(DefaultSimulator.class); /** + * When you create new simulator with specific SiMatrix you must + * overwrite this method to return you SiMatrix version + * @param context + * @return + */ + protected SiMatrix newSiMatrix(SimulationContext context) throws TopiaException { + return new SiMatrix(context); + } + + /** + * When you create new simulator with specific GravityModel you must + * overwrite this method to return you GravityModel version + * @param context + * @param siMatrix + * @return + */ + protected GravityModel newGravityModel(SimulationContext context, SiMatrix siMatrix) throws TopiaException, StorageException { + return new GravityModel(context, siMatrix); + } + + /** * Called by isis don't modify signature */ public void simulate(SimulationContext context) throws Exception { @@ -83,8 +104,8 @@ ResultManager resManager = context.getResultManager(); TopiaContext db = context.getDB(); - SiMatrix siMatrix = SiMatrix.getSiMatrix(context); - GravityModel gravityModel = new GravityModel(context, siMatrix); + SiMatrix siMatrix = newSiMatrix(context); + GravityModel gravityModel = newGravityModel(context, siMatrix); PopulationMonitor populationMonitor = context.getPopulationMonitor(); MetierMonitor metierMonitor = context.getMetierMonitor(); @@ -449,30 +470,10 @@ // this matrix is necessary for PopulationMonitor.holdCatch (reused in rule) MatrixND catchPerStrategyMetPerZonePop; - if (isEffortByCell(context)) { - abundance = siMatrix.matrixAbundance(N, pop, step); - catchPerStrategyMetPerZonePop = siMatrix - .matrixCatchPerStrategyMetPerZonePop(N, pop, step); - } else { // en zone - MatrixND matrixFishingMortality = siMatrix - .matrixFishingMortality(step, pop); - resManager.addResult(step, pop, matrixFishingMortality); + abundance = siMatrix.matrixAbundance(N, pop, step); + catchPerStrategyMetPerZonePop = siMatrix + .matrixCatchPerStrategyMetPerZone(N, pop, step); - abundance = siMatrix.matrixAbundance(N, pop, step, - matrixFishingMortality); - - // this matrix is necessary for matrixCatchPerStrategyMet - MatrixND catchRatePerStrategyMet = siMatrix - .matrixCatchRatePerStrategyMetPerZone(pop, step, - matrixFishingMortality); - resManager.addResult(step, pop, catchRatePerStrategyMet); - - catchPerStrategyMetPerZonePop = siMatrix - .matrixCatchPerStrategyMetPerZone(N, pop, step, - catchRatePerStrategyMet); - - } - popMon.holdCatch(pop, catchPerStrategyMetPerZonePop); resManager.addResult(step, pop, catchPerStrategyMetPerZonePop); @@ -484,35 +485,24 @@ resManager.addResult(step, pop, catchWeightPerStrategyMet); } - if (isEffortByCell(context)) { - MatrixND catchPerStrategyMetPerZoneMet = siMatrix - .matrixCatchPerStrategyMetPerZoneMet(N, pop, step); - resManager.addResult(step, pop, catchPerStrategyMetPerZoneMet); - - if (resManager - .isEnabled(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_MET)) { - MatrixND catchWeightPerStrategyMet = siMatrix - .matrixCatchWeightPerStrategyMetPerZoneMet(step, - pop, catchPerStrategyMetPerZoneMet); - resManager.addResult(step, pop, catchWeightPerStrategyMet); - } - } - if (resManager.isEnabled(ResultName.MATRIX_FISHING_MORTALITY_PER_GROUP) || resManager.isEnabled(ResultName.MATRIX_TOTAL_FISHING_MORTALITY)) { - MatrixND fishingMortalityPerGroup = siMatrix.fishingMortalityPerGroup(step, - pop, context.getResultManager()); + MatrixND fishingMortalityPerGroup = siMatrix.fishingMortalityPerGroup( + step, pop, context.getResultManager()); if (resManager.isEnabled(ResultName.MATRIX_FISHING_MORTALITY_PER_GROUP)) { resManager.addResult(step, pop, fishingMortalityPerGroup); } if (resManager.isEnabled(ResultName.MATRIX_TOTAL_FISHING_MORTALITY)) { - MatrixND totalFishingMortality = siMatrix.totalFishingMortality(step, pop, fishingMortalityPerGroup); + MatrixND totalFishingMortality = siMatrix.totalFishingMortality( + step, pop, fishingMortalityPerGroup); resManager.addResult(step, pop, totalFishingMortality); } } + siMatrix.computeMonthExtra(step, pop, N); + } else { // no strategies // compute only if fishing mortality =0 to apply Natural Mortality abundance = siMatrix.matrixAbundanceSsF(N, pop, step); Modified: trunk/simulators/SimulatorEffortByCell.java =================================================================== --- trunk/simulators/SimulatorEffortByCell.java 2014-12-03 15:48:52 UTC (rev 349) +++ trunk/simulators/SimulatorEffortByCell.java 2014-12-18 12:20:31 UTC (rev 350) @@ -26,29 +26,25 @@ import org.apache.commons.logging.LogFactory; import fr.ifremer.isisfish.simulator.SimulationContext; -import fr.ifremer.isisfish.simulator.SimulationParameter; -import fr.ifremer.isisfish.simulator.Simulator; +import scripts.SiMatrix; +import scripts.SiMatrixEffortByCell; +import org.nuiton.topia.TopiaException; + /** * Simulateur qui fixe la valeur de effortByCell a true pour force * l'utilisation des calculs par cellule plutot que par zone. * * @author poussin */ -public class SimulatorEffortByCell implements Simulator { +public class SimulatorEffortByCell extends DefaultSimulator { /** to use log facility, just put in your code: log.info("..."); */ static private Log log = LogFactory.getLog(SimulatorEffortByCell.class); - /** - * Called by isis don't modify signature - */ - public void simulate(SimulationContext context) throws Exception { - SimulationParameter param = context.getSimulationStorage().getParameter(); - param.getTagValue().put("effortByCell", "true"); - - DefaultSimulator simulator = new DefaultSimulator(); - simulator.simulate(context); + @Override + protected SiMatrix newSiMatrix(SimulationContext context) throws TopiaException { + return new SiMatrixEffortByCell(context); } }

1 0

r349 - trunk
by echatellier＠users.forge.codelutin.com Dec. 3, 2014

Dec. 3, 2014

Author: echatellier Date: 2014-12-03 15:48:52 +0000 (Wed, 03 Dec 2014) New Revision: 349 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/349 Log: Update versions Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-11-10 15:48:58 UTC (rev 348) +++ trunk/pom.xml 2014-12-03 15:48:52 UTC (rev 349) @@ -14,7 +14,7 @@ <packaging>jar</packaging>  - <version>4.3.2-SNAPSHOT</version> + <version>4.4.0-SNAPSHOT</version>  <description>Data for Isis-fish</description> @@ -36,7 +36,7 @@ <plugins> <plugin> <artifactId>maven-compiler-plugin</artifactId> - <version>3.1</version> + <version>3.2</version> <configuration> <source>1.7</source> <target>1.7</target> @@ -49,7 +49,7 @@ <plugin> <groupId>org.codehaus.mojo</groupId> <artifactId>exec-maven-plugin</artifactId> - <version>1.3.1</version> + <version>1.3.2</version> <executions> <execution> <goals> @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.3.2.0-SNAPSHOT</version> + <version>4.4.0.0-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies>

1 0

r348 - in trunk: . simulators
by kmorin＠users.forge.codelutin.com Nov. 10, 2014

Nov. 10, 2014

Author: kmorin Date: 2014-11-10 15:48:58 +0000 (Mon, 10 Nov 2014) New Revision: 348 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/348 Log: - upgrade isis-fish dependency version - merge Sigrid's modification on DefaultSimulator Modified: trunk/pom.xml trunk/simulators/DefaultSimulator.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-11-05 17:49:27 UTC (rev 347) +++ trunk/pom.xml 2014-11-10 15:48:58 UTC (rev 348) @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.3.1.1-SNAPSHOT</version> + <version>4.3.2.0-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies> Modified: trunk/simulators/DefaultSimulator.java =================================================================== --- trunk/simulators/DefaultSimulator.java 2014-11-05 17:49:27 UTC (rev 347) +++ trunk/simulators/DefaultSimulator.java 2014-11-10 15:48:58 UTC (rev 348) @@ -1,3 +1,4 @@ + /* * #%L * IsisFish data @@ -21,6 +22,7 @@ */ package simulators; +import fr.ifremer.isisfish.IsisFish; import fr.ifremer.isisfish.IsisFishException; import fr.ifremer.isisfish.entities.Metier; import fr.ifremer.isisfish.entities.Population; @@ -99,7 +101,7 @@ // reload context parameters with context.getDB() context param.reloadContextParameters(); - + // // Rule initialisation // @@ -108,7 +110,7 @@ for (Rule rule : rules) { rule.init(context); log.info("Rule " + rule.getClass().getSimpleName() - + " initialized"); + + " initialized"); } // @@ -120,7 +122,7 @@ // Simulation loop // while (step.getStep() < lastStep) { - + // // if user stop simulation before last year // @@ -151,9 +153,9 @@ if (siMatrix.getStrategies(step).size() > 0) { if (resManager.isEnabled(ResultName.MATRIX_NO_ACTIVITY)) { MatrixND mat = metierMonitor.getOrCreateNoActivity(step, - ResultName.MATRIX_NO_ACTIVITY, siMatrix + ResultName.MATRIX_NO_ACTIVITY, siMatrix .getStrategies(step), siMatrix - .getMetiers(step)); + .getMetiers(step)); resManager.addResult(step, mat); } } @@ -162,7 +164,7 @@ // Rule condition evaluation // control.setText("Evaluate rules conditions (" + rules.size() - + " rules)"); + + " rules)"); for (Rule rule : rules) { for (Metier metier : siMatrix.getMetiers(step)) { boolean active = false; @@ -171,14 +173,14 @@ } catch (Exception eee) { if (log.isWarnEnabled()) { log.warn("Can't evaluate rule condition for: " - + rule, eee); + + rule, eee); } } ruleMonitor.setEvaluationCondition(step, rule, metier, - active); + active); if (active) { log.info("Activate rule: " - + rule.getClass().getSimpleName()); + + rule.getClass().getSimpleName()); resManager.addActiveRule(step, rule); } } @@ -191,7 +193,7 @@ for (Rule rule : rules) { for (Metier metier : siMatrix.getMetiers(step)) { boolean condition = ruleMonitor.getEvalutionCondition(step, - rule, metier); + rule, metier); if (condition) { rule.preAction(context, step, metier); } @@ -213,7 +215,7 @@ for (Population pop : siMatrix.getPopulations(step)) { computeMonth(context, siMatrix, step, pop); } - + // // Add some result not population dependante // @@ -231,29 +233,12 @@ } if (resManager.isEnabled(ResultName.MATRIX_EFFORT_NOMINAL_PER_STRATEGY_MET)) { - MatrixND effortNominalPerStrategyMet = siMatrix.matrixEffortNominalPerStrategyMet(step); + MatrixND effortNominalPerStrategyMet = siMatrix.matrixEffortNominalPerStrategyMet(step); resManager.addResult(step, effortNominalPerStrategyMet); } - // - // Add economics results - // - if (!"false".equalsIgnoreCase(param.getTagValue().get( - "ecoResult"))) { - control.setText("Add economics results"); - saveGravityModel(step, resManager, gravityModel); - } } - // - // Add economics results - // - if (resManager.isEnabled(ResultName.MATRIX_PRICE)) { - for (Population pop : siMatrix.getPopulations(step)) { - MatrixND matPrice = siMatrix.matrixPrice(step, pop); - resManager.addResult(step, pop, matPrice); - } - } // // Rule post action @@ -297,7 +282,7 @@ .matrixDiscardWeightPerStrategyMetPerZonePop( pop, step, discard); resManager.addResult(step, pop, - discardWeightPerStrategyMet); + discardWeightPerStrategyMet); } } @@ -314,6 +299,26 @@ resManager.addResult(step, pop, landing); } } + + // + // Add economics results + // + + if (siMatrix.getStrategies(step).size() > 0) { + if (!"false".equalsIgnoreCase(param.getTagValue().get( + "ecoResult"))) { + control.setText("Add economics results"); + saveGravityModel(step, resManager, gravityModel); + } + } + + if (resManager.isEnabled(ResultName.MATRIX_PRICE)) { + for (Population pop : siMatrix.getPopulations(step)) { + MatrixND matPrice = siMatrix.matrixPrice(step, pop); + resManager.addResult(step, pop, matPrice); + } + } + } // @@ -339,12 +344,12 @@ protected boolean isEffortByCell(SimulationContext context) { boolean result = "true".equalsIgnoreCase(context.getSimulationStorage() - .getParameter().getTagValue().get("effortByCell")); + .getParameter().getTagValue().get("effortByCell")); return result; } protected void computeMonth(SimulationContext context, SiMatrix siMatrix, - TimeStep step, Population pop) throws IsisFishException, TopiaException { + TimeStep step, Population pop) throws IsisFishException, TopiaException { // to add result ResultManager resManager = context.getResultManager(); @@ -353,8 +358,8 @@ if (log.isInfoEnabled()) { log.info("====================== begin " + step + " - " + pop - + " =========================== " - + System.currentTimeMillis()); + + " =========================== " + + System.currentTimeMillis()); log.info("N: " + N); } @@ -427,7 +432,7 @@ if (resManager.isEnabled(ResultName.MATRIX_ABUNDANCE_BEGIN_MONTH)) { MatrixND abondanceBM = siMatrix.matrixAbondanceBeginMonth(N, pop, - step); + step); resManager.addResult(step, pop, abondanceBM); } @@ -454,17 +459,17 @@ resManager.addResult(step, pop, matrixFishingMortality); abundance = siMatrix.matrixAbundance(N, pop, step, - matrixFishingMortality); + matrixFishingMortality); // this matrix is necessary for matrixCatchPerStrategyMet MatrixND catchRatePerStrategyMet = siMatrix .matrixCatchRatePerStrategyMetPerZone(pop, step, - matrixFishingMortality); + matrixFishingMortality); resManager.addResult(step, pop, catchRatePerStrategyMet); catchPerStrategyMetPerZonePop = siMatrix .matrixCatchPerStrategyMetPerZone(N, pop, step, - catchRatePerStrategyMet); + catchRatePerStrategyMet); } @@ -475,9 +480,9 @@ .isEnabled(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_POP)) { MatrixND catchWeightPerStrategyMet = siMatrix .matrixCatchWeightPerStrategyMetPerZonePop(step, pop, - catchPerStrategyMetPerZonePop); + catchPerStrategyMetPerZonePop); resManager.addResult(step, pop, catchWeightPerStrategyMet); - } + } if (isEffortByCell(context)) { MatrixND catchPerStrategyMetPerZoneMet = siMatrix @@ -488,7 +493,7 @@ .isEnabled(ResultName.MATRIX_CATCH_WEIGHT_PER_STRATEGY_MET_PER_ZONE_MET)) { MatrixND catchWeightPerStrategyMet = siMatrix .matrixCatchWeightPerStrategyMetPerZoneMet(step, - pop, catchPerStrategyMetPerZoneMet); + pop, catchPerStrategyMetPerZoneMet); resManager.addResult(step, pop, catchWeightPerStrategyMet); } } @@ -496,12 +501,12 @@ if (resManager.isEnabled(ResultName.MATRIX_FISHING_MORTALITY_PER_GROUP) || resManager.isEnabled(ResultName.MATRIX_TOTAL_FISHING_MORTALITY)) { MatrixND fishingMortalityPerGroup = siMatrix.fishingMortalityPerGroup(step, - pop, context.getResultManager()); + pop, context.getResultManager()); if (resManager.isEnabled(ResultName.MATRIX_FISHING_MORTALITY_PER_GROUP)) { resManager.addResult(step, pop, fishingMortalityPerGroup); } - + if (resManager.isEnabled(ResultName.MATRIX_TOTAL_FISHING_MORTALITY)) { MatrixND totalFishingMortality = siMatrix.totalFishingMortality(step, pop, fishingMortalityPerGroup); resManager.addResult(step, pop, totalFishingMortality); @@ -518,7 +523,7 @@ popMon.setN(pop, abundance); log.debug("====================== end " + step + " - " + pop - + " ==========================="); + + " ==========================="); } @@ -529,7 +534,7 @@ * @throws TopiaException */ private void saveGravityModel(TimeStep step, ResultManager resManager, - GravityModel gravityModel) throws IsisFishException, TopiaException { + GravityModel gravityModel) throws IsisFishException, TopiaException { if (resManager .isEnabled(ResultName.MATRIX_FISHING_TIME_PER_MONTH_PER_VESSEL)) { MatrixND mat = gravityModel

1 0

r347 - in trunk: . simulators
by kmorin＠users.forge.codelutin.com Nov. 5, 2014

Nov. 5, 2014

Author: kmorin Date: 2014-11-05 18:49:27 +0100 (Wed, 05 Nov 2014) New Revision: 347 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/347 Log: fixes #5932 Parametrer les simulations en mois Modified: trunk/pom.xml trunk/simulators/DefaultSimulator.java Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-10-08 11:13:07 UTC (rev 346) +++ trunk/pom.xml 2014-11-05 17:49:27 UTC (rev 347) @@ -74,7 +74,7 @@ <dependency> <groupId>fr.ifremer</groupId> <artifactId>isis-fish</artifactId> - <version>4.3.1.0</version> + <version>4.3.1.1-SNAPSHOT</version> <scope>compile</scope> </dependency> </dependencies> Modified: trunk/simulators/DefaultSimulator.java =================================================================== --- trunk/simulators/DefaultSimulator.java 2014-10-08 11:13:07 UTC (rev 346) +++ trunk/simulators/DefaultSimulator.java 2014-11-05 17:49:27 UTC (rev 347) @@ -75,8 +75,7 @@ SimulationParameter param = context.getSimulationStorage() .getParameter(); SimulationControl control = context.getSimulationControl(); - int lastYear = param.getNumberOfYear(); - int lastStep = lastYear * Month.NUMBER_OF_MONTH; + int lastStep = param.getNumberOfMonths(); TimeStep step = control.getStep(); ResultManager resManager = context.getResultManager();

1 0

r346 - in tags/4.3.1: scripts simulators
by echatellier＠users.forge.codelutin.com Oct. 8, 2014

Oct. 8, 2014

Author: echatellier Date: 2014-10-08 13:13:07 +0200 (Wed, 08 Oct 2014) New Revision: 346 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/346 Log: Use result manager Modified: tags/4.3.1/scripts/SiMatrix.java tags/4.3.1/simulators/DefaultSimulator.java Modified: tags/4.3.1/scripts/SiMatrix.java =================================================================== --- tags/4.3.1/scripts/SiMatrix.java 2014-10-08 11:00:58 UTC (rev 345) +++ tags/4.3.1/scripts/SiMatrix.java 2014-10-08 11:13:07 UTC (rev 346) @@ -55,10 +55,10 @@ import fr.ifremer.isisfish.entities.StrategyMonthInfo; import fr.ifremer.isisfish.entities.Zone; import fr.ifremer.isisfish.entities.ZoneDAO; +import fr.ifremer.isisfish.simulator.ResultManager; import fr.ifremer.isisfish.simulator.SimulationContext; +import fr.ifremer.isisfish.types.Month; import fr.ifremer.isisfish.types.TimeStep; -import fr.ifremer.isisfish.types.Month; -import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.util.Nocache; /** @@ -1891,7 +1891,7 @@ * @param pop population * @return Fishing mortality per group per year (computed in December) */ - public MatrixND fishingMortalityPerGroup(TimeStep step, Population pop, ResultStorage resManager) throws TopiaException { + public MatrixND fishingMortalityPerGroup(TimeStep step, Population pop, ResultManager resManager) throws TopiaException { double Fgroup = 0; double Cgroup = 0; double Mgroup = 0; Modified: tags/4.3.1/simulators/DefaultSimulator.java =================================================================== --- tags/4.3.1/simulators/DefaultSimulator.java 2014-10-08 11:00:58 UTC (rev 345) +++ tags/4.3.1/simulators/DefaultSimulator.java 2014-10-08 11:13:07 UTC (rev 346) @@ -499,7 +499,7 @@ if (resManager.isEnabled(ResultName.MATRIX_FISHING_MORTALITY_PER_GROUP) || resManager.isEnabled(ResultName.MATRIX_TOTAL_FISHING_MORTALITY)) { MatrixND fishingMortalityPerGroup = siMatrix.fishingMortalityPerGroup(step, - pop, context.getSimulationStorage().getResultStorage()); + pop, context.getResultManager()); if (resManager.isEnabled(ResultName.MATRIX_FISHING_MORTALITY_PER_GROUP)) { resManager.addResult(step, pop, fishingMortalityPerGroup);

1 0

r345 - in trunk: scripts simulators
by echatellier＠users.forge.codelutin.com Oct. 8, 2014

Oct. 8, 2014

Author: echatellier Date: 2014-10-08 13:00:58 +0200 (Wed, 08 Oct 2014) New Revision: 345 Url: http://forge.codelutin.com/projects/isis-fish-data/repository/revisions/345 Log: Use result manager Modified: trunk/scripts/SiMatrix.java trunk/simulators/DefaultSimulator.java Modified: trunk/scripts/SiMatrix.java =================================================================== --- trunk/scripts/SiMatrix.java 2014-10-08 10:20:56 UTC (rev 344) +++ trunk/scripts/SiMatrix.java 2014-10-08 11:00:58 UTC (rev 345) @@ -55,10 +55,10 @@ import fr.ifremer.isisfish.entities.StrategyMonthInfo; import fr.ifremer.isisfish.entities.Zone; import fr.ifremer.isisfish.entities.ZoneDAO; +import fr.ifremer.isisfish.simulator.ResultManager; import fr.ifremer.isisfish.simulator.SimulationContext; +import fr.ifremer.isisfish.types.Month; import fr.ifremer.isisfish.types.TimeStep; -import fr.ifremer.isisfish.types.Month; -import fr.ifremer.isisfish.datastore.ResultStorage; import fr.ifremer.isisfish.util.Nocache; /** @@ -1891,7 +1891,7 @@ * @param pop population * @return Fishing mortality per group per year (computed in December) */ - public MatrixND fishingMortalityPerGroup(TimeStep step, Population pop, ResultStorage resManager) throws TopiaException { + public MatrixND fishingMortalityPerGroup(TimeStep step, Population pop, ResultManager resManager) throws TopiaException { double Fgroup = 0; double Cgroup = 0; double Mgroup = 0; @@ -1913,12 +1913,12 @@ for (TimeStep loopstep = new TimeStep(step.getYear() * 12); loopstep.beforeOrEquals(step); loopstep=loopstep.next()) { // On fait cette boucle pour contourner les aspects de cache qui font que les resultats ne sont pas recuperes - //s'ils ont deja ete calcules une fois (meme s'ils ont change depuis) + // s'ils ont deja ete calcules une fois (meme s'ils ont change depuis) // beforeOrEquals sert a bien prendre Decembre aussi MatrixND catchPerStrategyTemp = resManager.getMatrix(loopstep, pop, ResultName.MATRIX_CATCH_PER_STRATEGY_MET_PER_ZONE_POP); if (catchPerStrategy == null) { - catchPerStrategy = catchPerStrategyTemp.clone(); + catchPerStrategy = catchPerStrategyTemp.copy(); // On clone la matrice car si on fait les operations sur celle contenue dans le cache on la modifie et donc on recupere des resultats faux. } else { catchPerStrategy = catchPerStrategy.add(catchPerStrategyTemp); // Pour avoir la somme des captures sur les 12 mois Modified: trunk/simulators/DefaultSimulator.java =================================================================== --- trunk/simulators/DefaultSimulator.java 2014-10-08 10:20:56 UTC (rev 344) +++ trunk/simulators/DefaultSimulator.java 2014-10-08 11:00:58 UTC (rev 345) @@ -497,7 +497,7 @@ if (resManager.isEnabled(ResultName.MATRIX_FISHING_MORTALITY_PER_GROUP) || resManager.isEnabled(ResultName.MATRIX_TOTAL_FISHING_MORTALITY)) { MatrixND fishingMortalityPerGroup = siMatrix.fishingMortalityPerGroup(step, - pop, context.getSimulationStorage().getResultStorage()); + pop, context.getResultManager()); if (resManager.isEnabled(ResultName.MATRIX_FISHING_MORTALITY_PER_GROUP)) { resManager.addResult(step, pop, fishingMortalityPerGroup);

1 0